secrets
by nuttynat999
Summary: John's memory has always drawn a blank in relation to his past leaving a mystery and his fair share of secrets, what would happen if he should have to face to face with aspects of his past he doesn't remember and some of his secrets coming to light.
1. Chapter 1

Secrets

Stargate atlantis/Macgyver crossover

Chapter one:to

For John Atlantis was his life, he could honestly say he couldn't remember much before joining the Air force so therefore the Air force and the SGC was pretty much his life. But something nagged him from time to time there was this hole, a constant gap in his memory, it all started when he woke up in the hospital bed all those years ago, no one knew who he was or where he came from and no one came to claim him so he kind of accepted it and moved on. That's when he met the Sheppard family, they were a nice family but not is own, they kind of adopted him one day after they got to know in the hospital. John always thought they took pity on him because he was alone and had nowhere to go. However, that was the past but it doesn't mean he doesn't think about it every now and again. They always seemed to be the same questions, Was he in an accident? did he have family? was John his real name or was his name something else? John he had to admit just seemed right at the time, but about all these things he seemed to know, this was the biggest mystery why did he have this strange affinity for numbers and science perhaps one day he would pick up the courage to find out.

John wouldn't admit it to Rodney or Elizabeth or to anyone else in the SGC though, the fact that he did actually understand a lot of what the scientists in Atlantis were doing and in fact from time to time would love to jump in and tell them when they were wrong and correct their mistakes (for they made so many) especially McKay and his ego, but something held him back. Was it fear, was he more comfortable hiding behind this mask that he had created to protect himself. John wasn't sure but he knew that if they took him away from flying and his command and shoved him a lab he'll hate it and go stir crazy. Lost in thought once again it was the sound of a Czech accent that made him look up, Radek was arguing with Rodney again, he chuckled to himself when he heard Radek call Rodney '**dobrý zprostředkující zařízení šprýmař'** in his native language. Where this ability came from to understand him he didn't know but it was certainly helpful from time to time and Radek wasn't the only one he could understand but he would keep that to himself for now because it would give him the element of surprise, anyway John prodded on with his paperwork and for now these questions were just going to have to wait in line, for he had a lot to do today, and the Deadalus was due arrive anytime soon so dwelling on the past wasn't going to help keep to his schedule.

Pushing these thoughts back into the depth of his mind John smiled as he finished the last pages turning his thoughts to that of flying and his trip in the jumper in the mainland with Teyla after his meeting with Elizabeth later this afternoon. But first he had to meet and greet his newest recruits arriving on the Deadalus, that was always an interesting occasion.

Translation "**dobrý zprostředkující zařízení šprýmař**"– big headed buffoon


	2. Chapter 2

Chapter Two:

Alison Mallory was new to the city she had just been recruited by the SGC by the science department, she still couldn't believe she was in another galaxy and the truth of the matter it all seemed a little science fiction even though she had just spent the last three days on the ship Deadalus travelling to Atlantis.

Alison was to be apart of Dr Rodney Mckay science team he had heard of him but they were only rumours and not good ones at that. Even people at the SGC had repeatedly informed her that he was a genius but had a bad temper and a vicious mouth, so she was silently dreading the final meeting. Her speciality was temporal physics when they first approached her she couldn't understand why an underground military facility would be so interested in her particular field, but what they were offering she couldn't refuse, (a large grant and a chance to explore new worlds hell how can you say no to that) it did however come with a clause that she had to sign a classified non-disclosure paper, but it also meant that the Phoenix Foundation were now involved in the programme something she had highly recommended and pushed for before she signed, Macgyver would love this as she smiled to herself.

Thinking back to the day she was introduced to the Stargate Programme she felt like she was completely over her head but General O'Neill seemed ok, and Dr Jackson was wonderful she couldn't help wondering about the other people that she had heard about. Dr Elizabeth Weir the civilian commander of the base, Alison had actually met her once whilst she was contracted at the Phoenix Foundation, Elizabeth had been called in by Pete Thorton the head of the Phoenix Foundation to mediate between to technological companies that highly suspicious of each other and were undergoing a merger. The Phoenix group had been called in to support the merger and to highlight the new science division that they had funded that would be the centre and base of their new merged company if only they could get over the hostility. Alison remembered liking the woman she was headstrong and fair and actually managed to get the two groups to sit down together and reach an agreement that in itself was hard work so she was much respected in her eyes.

This other one the head of the military constituent intrigued her though Lt Colonel John Sheppard there was no picture unfortunately and she hadn't managed to get her hands on one, so she was going in blind on this one. However, she had gained a idea from other military personnel that he was highly respected which was highly unusual considering a lot of them were marines and he was Air force so he must have done something right. She was also informed he was fair and had been at Atlantis since the beginning so be aware that what he says goes, especially in relation to military protocol and the safety of the civilians on the base. From what she had heard she couldn't actually wait to meet him especially since there was also rumours he was designated 'Kirk of the Pegasus galaxy' by Dr McKay and some to the female constituent so he must also be quite a looker she did seem to remember a few blushes when she asked.

Anyhow she had arrived the Deadalus had just docked and she gathered up her belonging joining the other marines and scientist as they gathered at the docking bay. As the door opened she felt herself being herded down into the main area where they were a number of personnel waiting to collect them and take them to their designated areas. As she walked down the platform she was viciously pushed out the way causing her fall by one of the new marines, isn't he eager she thought but the only words that seemed to come out was "oww" he stopped and looked at her "sorry madam" well she didn't expect that. He took arm and helped her back up and again apologised. Alison seeing no harm done dusted herself off "its ok no harm done" she replied. The young marine smiled "I'm just a little overexcited" he explained "I wanted to get down and meet the legendry Colonel Sheppard you know we've all heard about at the SGC and his missions I guess it was now were here my manners went out of the window". Alison looked at him and smiled and nodded understandably "I know I've heard some of his exploits, I understand and accept your apology". The young marine only blushed and quickly took some of her belongings "let me help you madam it's the least I can do, anyway the Colonel always says we need to look after our scientists". Handing over her case she thanked him, this Colonel Sheppard only seemed to intrigue her all the more, and from the sound of the shouting "scientists over to Dr Mckay, marines and other military personnel over to Major Lorne and Colonel Sheppard" she just might get to meet him yet


	3. Chapter 3

Chapter 3:

John Sheppard could hear the gathering crowd in the docking bay from his office, setting his pen down he stood and went to his window and looked over the crowd of people now standing in the main docking bay. "Right John lets get this over with he said to himself" stepping out of his office he headed over to the balcony where Lorne was standing with a clipboard in deep conversation with a member of the Deadalus crew, John stared obviously the internity he thought, heading over. "Sir" Lorne quickly stated as he snapped to attention, "are we ready" drawled John in a lazy tone "yep ready and waiting not patiently mind you" john looked at him expectantly 'don't look to excited' he thought to himself. Lorne looked at him and explained "there seems to be a bit of hero worship going on sir, it appears the rumour mill as been at it again and there dying to meet you" he laughed . John shuddered only making Lorne laugh all the more "damn SGC and gossip makers". Turning his attention to the crowd below John sighed "here we go, lets get this over with. I've got one more meeting and then a date with a jumper." Smiling he headed over, by now they should be there groups "lets meet and greet" Lorne smiled and headed over to join him.

Alison was waiting expectedly Dr McKay had given his lecture on being the best and the brightest and not stuffing up and now she was waiting for this final meet and greet with the base commanders before going to their living quarters. To be honest she was looking forward to this. Not a moment to soon she heard Dr Weir shout down and introduce herself before she came face to face with a tall lanky man with wild hair she could hear Dr Weir in the background introducing him as Colonel Sheppard but their was something about him that was off, no it couldn't be she thought to herself she looked again but before she could distinguish his face he had moved away and she actually found herself face to face with the soldier known as Lorne looking at her strangely as she stood alone in the docking bay.

"Are you ok doc?" he found himself asking, she looked at him confused "yeah! yeah sorry!" she replied "you just seemed a little out of it there" "yeah I am fine" was all she could say trying to get his face out of her mind, was she wrong she thought, had she made a mistake. Lorne seemed to pick up on this confusion, "he's a little hard to get your hand around isn't he?" he asked "I remember the first time I met him" he continued "I wasn't sure what to think about as well but he grows on ya I assure you" she continue to stare at him, "come on doc lets get you to your room, I'm Major Lorne by the way." Shaking away her confusion she gathered herself and apologised "I'm sorry my names Alison, Alison Mallory." "Nice to meet ya" he replied politely, the rest of the walk was silent she just seemed to be thinking about the man she had seen earlier he seemed so familiar, she didn't mean to be rude but Sheppard was all she could think about right now. Lorne stopped outside her designated room after checking with the list he had managed to find and wished her good day before leaving her lost in thought. Alison entered her room dropping her things to the floor, she sat down and thought about how she was going to approach this issue. How was she going to find out more about this Sheppard and was this Sheppard ….John Sinclair, MacGyver's nephew that went missing 15 years ago whilst on a mission, a mission that he and herself was on whilst working for the Phoenix Foundation.

Reviews much appreciated however, this is my first fanfic so please be patient with me.


	4. secrets Chapter 4

John stood on the balcony and looked at the crowd below 'right here we go' he thought 'that my cue.' John heard Elizabeth finish her little speech and prepped himself. "And now I pass you over to Colonel Sheppard" Elizabeth stepped back as he stepped forward, God they looked eager. "Good afternoon Ladies and Gentleman as you already know my name is Colonel Sheppard and your military Co what I want to do is ignore everything you have ever been told about Atlantis and the Pegasus Galaxy, and listen up. There is nothing like this place, Atlantis is a wondrous place but a dangerous one so no messing around, any problems please approach your section leaders; if you can't approach them my door is always open to everyone. You will all be designated rooms and some of you may end up on an off world team, those of you that do please remember to follow your team leaders and follow their command like I am giving you one personally, that could make the difference between life and death. We have many enemies the Wraith are all but one, but we also have many friends, so be aware of your surroundings. I won't bore you anymore, ladies and gentlemen you have been chosen because you are the best so congratulations and welcome to Atlantis, fall out." There was massive "Hoorah" from below and they quickly dispersed.

John quickly took this has his cue to leave and headed into Elizabeth's office as soon as he got this meeting over with the better and the quicker he could be on that jumper heading to the mainland. Elizabeth was sat at her desk with a console in her hand she looked as John entered "well John that was inspirational as always" "well you know me always liked to set the trend" he laughed Elizabeth put her console down and smiled.

The meeting was long and boring as always, Caldwell attending the meeting didn't help as John had to look as attentive as ever. 'God kill me now he thought' rolling his eyes especially because Caldwell seemed to be looking at him which was every two minutes. The torture soon ended and John quickly stood thanked Elizabeth and Caldwell and fled the room quickly heading to the jumper bay where he promised to meet Telya. However, just as he was about to enter the transporters he could hear McKay behind him calling for him "Sheppard, Sheppard, god damn it slow down…. Stop ignoring me…" he almost seemed to be running now as his voice was getting louder. "Don't you dare colonel get in that thing this is important…." John stopped just as he was about in get in and turned to the irritable scientist "this better be good, I've got places to be McKay" "well its almost important colonel but you flyboys don't understand the meaning of things like that". John just frowned at him "don't push it McKay" "now what's got your back up" "Haha, very funny colonel and that would be nothing only that you need to come with me to the chair room and help me to sort out the security net, Atlantis won't let me remotely activate the security protocol you wanted me to put in place." "Can't it wait, no wait can't you use Carson". McKay looked at him with an annoyed look "you know what, no! Carson couldn't do it Atlantis wouldn't let him access the system kept asking for higher authority, hence the reason why 'asking you!" he highlighted. John frowned turning to look at the welcoming transporter that would take him away and turn back to McKay "ok, ok I'm coming" decision made turning away from the transporter following closely behind McKay, tapping his earpiece "Telya, come in" "yes John" "Look your going to have to go to the mainland without me, Rodney needs me to access the chair and doesn't know how long it is going to take, ask Stratmore to take you over, Ill pick you up in three days or head over when I can ok" "Ok John".

John headed to the chair room where Rodney was waiting "right lets get this over with" sitting down.

The chair activated straight away and John immediately went to the area Rodney asks him to enter. John pushed his thoughts to Atlantis mainframe asking for access, Atlantis was hesitant at first "access denied" but then suddenly allowed him access "access permitted commander John" he heard in his mind. John though nothing of it and continued Atlantis then quickly started pushing pictures and diagrams and other data into his mind, "Right Rodney what do you need me to do". Rodney looked at him "you're in already, oh right, I need to you to access the security mainframe and get Atlantis to allow me access." John pushed his way through the vast amount of data and made his way to the security protocol there he asked Atlantis to allow Rodney access to the mainframe from his remote console so he could make some changes. Atlantis quickly did as she was asked and allowed Rodney access, John could hear Rodney in the background "wow, this is stuff I've never had access to before, John what did you do" as the data continued to flash onto his screen …he continued to mutter to himself whilst John shut the chair down feeling exhausted John just remained sat down and closed his eyes slipping into unconsciousness. Rodney didn't notice the colonel slipping into unconsciousness until he was calling for him especially because there was a annoying beeping sound coming from the chair and got no reply "colonel will you stop ignoring me and turn that alarm of, its actually getting to get on my …" stopping mid speech as he looked up from his console and found himself looking at a very unconsciousness colonel and a red light surrounding his still form "oh crap".


	5. Chapter 5

Alison had been unpacking her belonging this issue with Colonel Sheppard was still on her mind what could she do, I mean what if I'm wrong she heard her telling herself. To be honest she had kind of accepted that he was dead there was no news for all that time so why would he be suddenly be alive now.

Getting ready for her first shift she decided that she would ask around maybe get some background information on the man wouldn't do any harm. The mission when he went missing suddenly swarmed back into her mind where did that come from she thought, it hadn't been an easy one and to be honest she wanted to forget about it all over again.

15 years earlier….

"John you know we have to be careful if they suspect we dead" , "Don't worry Ally, us meeting up, I'll just say that I've got a sexual interest in ya!, you know what Carlos is like, he's sex mad he probably even ask for the glory details, the man's sick." "Well he is in the sex slave trade" John looked at her and smiled which was hard considering all he's seen the last few months "come on I got some intel for you to give Pete and Mac." Alison sat down ready on the bed and John started to give her all the glory details of the next meeting and sale of sex slaves Carlos had planned, she worried for him, sometimes he come with bruises and strange marks on his body and when she asked he would just shrugged her off "its nothing." Today was no different only when he was talking he hands were quite animated and that's when she saw the burn marks around his wrist where its looks like his hands had been bound with rope, John hadn't noticed her eyes scaring at his wrists, until she grabbed his wrist "ouch" he announced "what this?", before he could pull away "and don't say nothing" he looked down and avoided her graze "what's going on John and this isn't the first time" John stepped back like a frightened deer "leave it alone Ally it will be over soon anyway" "no John you will tell me now or so help me God, I'll …I'll contact Mac" John froze "no, don't" "Look Carlos got a bit rough that's all". "What do you mean? There is something you're not telling me John, look at me..." John looked up at her and all she could see was shame and pain. "What did he do John?" John avoided the question and starting mumbling. "He told me I was beautiful the most beautiful thing he had ever come across, he touched me and then kissed me, I didn't know what to do you know, and I saw what he did with the women that rejected him so I didn't fight him." John stopped and went quiet the atmosphere suddenly went cold "Fight what, what he do…John?" John remained quiet she got up and approached him and touched his arm gently she could feel him trembling.

"John" as she turned him "What did he do?" more determined. John turned and stared into her eyes, "he got his men to tie me to the bed and then he raped me and then they took turns," Alison stepped back from John in shock she placed her hand over mouth like she was going to be sick John recoiled thinking she was sickened with him "Oh John!" suddenly seeing his reaction she grabbed him and pulled him into a hug "oh John it isn't you, I'm so sorry it wasn't to suppose to happen." She was crying now and so was John "we're pulling you out, God this isn't going to happen to you again." But John stopped her "you can't not yet there's another shipment, what happened to me is happening to hundreds of women because of him, no let me finish" before she could but in. "Let me catch him with this shipment, then I'm done I'll see a counsellor, I'll do whatever, just let me finish." "John" "Please" he begged. "Ok, but if you feel anything wrong get out of there, promise" "I promise and thank you" He grabbed his coat and headed to the door, "will you be ok" she asked "no, but I'll survive and hopefully he won't be interested in me tonight with guests being at his house and all." She quickly held him and kissed, and John left.

Present…

That was the last time she saw him that night and god she felt guilty why didn't she stop him. MacGyver had forgiven her saying that was the way he was, he even continued to invite her every year to his home, and how he did it she didn't know. But if it was John how she could pay back all those years. The only problem he looked like him, but he didn't seem like him, he was care free, happy, and showed no sign of abuse or even recognising her though she was in a crowd but surely he would have recognised her from her file especially if the Phoenix foundation was written it as a reference. There was more to it and she was going to find out.

Suddenly she heard an announcement, "Med team to chair room, the colonels down, not sure what's wrong" "not again" she whispered jumping up and heading out the door. Grabbing the nearest person she could find "excuse me where is the chair room." The young woman turned and pointed "down the hall, keep going fifth turning on the right you can't miss it."

Giving quick thanks she ran down the hall only to be met with numerous medics and a gurney with a very unconsciousness colonel on it. "What happened" she asked "we don't know, look we've got to go" heading away she suddenly found herself face to face with a very worried Rodney McKay looking at her with a warily "and who are you?" "Sorry, I'm Alison Mallory, I'm on your team" Rodney continued to look at with a look confusion and contempt "You know your new Astrophysicist" Alison was little unnerved she wasn't used to people staring at her like that. "Oh yes, yes the Phoenix foundation, but what you doing here" she looked at his frown "I heard on the intercom and just wanted to see how he was" Rodney looked her dumbly "not another one, he never ceases to amaze me, Kirk and his genes, he only has to fall unconscious and every woman on the planet wants to see how he is." She just stared at him as he wandered away still muttering to him self completely forgetting she was there, she could hear the odd comments about how the colonel is unbelievable, but she could see he was worried for him, maybe that's how he deals with it she thought. "Well it was nice meeting you" she shouted, "yes, yes" was all she heard.

Well now I have to meet him she thought to herself, as she turned and headed back to her room, a John Sheppard on her mind.


	6. Chapter 6

John awoke with the sound of beeping next to his head and he was sure he could hear Carson muttering away in the back ground he was definitely in the infirmary. "What happened?" he heard himself ask and suddenly found himself in the presence of Rodney McKay shouting Carson over to his bed. "Carson he's awake, get over here and use your voodoo on him and make sure he's ok" "I'm fine McKay" he winced god that was a killer headache "but I won't be if you keep shouting like that" "Fine be like that, its your own fault anyway if you weren't well you should of said rather then letting me find you dead almost, you scared me half to death." "I'm fine Rodney! I don't know what happened I just felt exhausted" "Ay son you were, your readings were off the chart, whatever you did you stupid sod, caused your body to collapse" Carson added as he wandered over. "How's your head?" "And don't lie to me Colonel otherwise I'm going to keep you in" John went to give a witty retort but thought better of it Carson looked rather pissed. "Sore, got a killer headache" he answered honestly. Carson wandered over to the medicine cabinet and returned with some painkillers "take these and then rest for a bit, ill let you out later this afternoon" but before John could reply "no sooner". "Fine" closing his eyes, "and Rodney out, John needs his sleep."

Carson then wandered away to deal with other patients before leaving Rodney looks at John "what happened John? I mean one minute I 'm getting all this cool stuff you were fine and then next thing I know, there you are unconsciousness and Atlantis shuts down" John looks at him confused "what? I don't know Rodney but!" John lowers himself to a whisper "I could hear her Rodney she was talking to me, you know welcoming me home". Rodney looked at him with a surprised look, "I don't think that's even possible John, you sure you weren't just imagining it" "No Rodney, she called me commander" .Rodney just looked stumped "I don't know John but maybe we should just keep this between us for now" as Rodney was about to open his mouth again Carson began to wander back over and seeing his face and it wasn't a happy one Rodney quickly retorted "catch you later John, I'm not messing with the voodoo man I might find myself in a bed next to you" as he eyed Carson getting closer, "sure Rodney see ya later" with that Rodney quickly left and John found himself alone, closing his eyes, he got some sleep.

Rodney headed to the lab, now John was sorted and ok he could get on with his work, but he would discuss this issue with Atlantis later on the implications "wow" he thought to himself. He just wanted to examine the data on his console from the chair room earlier. As he entered he found Zelenka working on his equations on the jumper systems he was creating¸ and everyone else seemed to be in their own world, well that was easy he thought everyone seems to know what they were doing. However, as he ventured in further he found himself coming in contact with that small dark haired woman from outside the chair room he met earlier what was her name yes "Alison" " Yes oh , sorry Dr McKay" "what are you doing?" he asked her as he couldn't quite work out what she was doing apart from being in his way. "I'm examining the equations to this theory on temporal rift there is something not quite right" Rodney gave a little snort "mmmm… and what do think is wrong, I'll have you know its perfect" she just turned back to him and then back to the equations in front of her, "they just seem too perfect, like there is a section missing" Rodney had heard enough "look miss busybody why don't you buzz off and get with whatever you do rather then nosing into my equations, not right indeed" he snorted once again and brushed her off. "Fine" as she wandered over to doctor Zelenka "is he always like that" she asked. "Yes" was all she got. Alison sat down next to him and got out her console and began to examine the list of tasks she had scheduled for the day, starting casual conversation she decided it the perfect opportunity to find out more about Colonel Sheppard.

"So Dr Zelenka got a first name" he turned to look at her "Radek" he replied "and yes that is fine" she stared at him " to use my first name, no" "oh yes, so what's it like to work for the great Rodney McKay" Radek snorted but honestly answered " it is not all bad, he is what you call egomaniac but he know what talking about, he has changed though he has mellowed I suppose he was much worse". Alison snorted at that "no, he has I think is because of his friendship with Colonel Sheppard." Alison looked at him to further elaborate. "Colonel Sheppard asked Rodney to be on his team, he laughs at Rodney's jokes and also is the only person who can deal with Rodney when he like he is today." "Oh" she replied "it is best on days like today to stay out of his way he was scared for the colonel and so he is extra moody and nasty." Alison couldn't agree more. "So tell me about Colonel Sheppard, it seems he is very popular" Radek looked to her as to say it's true. "The colonel is important to us, he would do anything for his men and the scientists, he would never leave a man behind. The colonel is very protective, but he is a very secretive man I think he is more intelligent then he lets on" Alison looks at him strangely, "the colonel would never say it is his idea but I have seen the colonel solve a problem and give Rodney the credit." Interesting she thought. "Does Rodney know, I mean surely he's noticed" "I think he has some idea but John is his friend, he lets him have his secrets, Rodney told me once that he was explaining something to John once about wormholes and Rodney told me that he could sense John understood everything but pretended he didn't".

This information was important Alison sensed John Sinclair was brilliant his understanding of science and maths was far beyond her own and MacGyver's he was a prodigy, this information only furthered her opinion that John Sheppard was in fact John Sinclair but she needed more proof. With that Alison went back to her thoughts maybe it was time to meet John Sheppard and find out what happened all those years ago, but first she needed to gather evidence and let him get well.


	7. Chapter 7

Chapter 7

'God he wanted out of here', but after Rodney left John found himself feeling worse, he had managed to get a few hours sleep but all of a sudden he felt ill and he had the strangest nightmare or whatever it was, feeling unwell he found himself dragging himself over to the nearest bin, that when Carson came over "you alright son." "No" was all he could reply as he threw up everything from in his stomach. Carson could feel the heat coming of him, what had changed all of a sudden, "let's get you back into bed lad" Carson went to touch him and John suddenly felt claustrophobic "DON'T TOUCH ME" he heard himself shout, but why he didn't know, Carson seemed to reel back in shock "John you ok, John look at me!" John turned to look at him but even though he could hear Carson voice there was another image, another face looking at him and it wasn't Carson, this face frightened him, did he know him, a number of realisations seemed to hit him all at once, whoever this person was he was seeing he didn't like him and he had gotten a feeling of pain and dread 'he had hurt me' he realised as he recognised these feelings, these were similar feelings he had experienced from time in Iraq. Suddenly there was a rush of nurses coming into the room hearing everything going on from the other room, Carson firmly commanded "stay back, let me deal with this" John found himself backing away and found backed himself backed into a corner against a wall Carson placed his hands up in a defensive manner. John couldn't think straight, "what's happening to me?" he heard himself saying out loud, the image of the man got stronger and suddenly John felt pain down below and a sense of panic hit him.

The Shock and realisation suddenly hit him "he raped me" he whispered "he wouldn't stop" John found himself saying, Carson recoiled "what?" the nurses grasped Carson ignored returning his attention back to his friend, he could mentally hit himself 'of course' he though the signs were there. Carson suddenly went into friend mode, 'he's in a flashback, God I'm so stupid' he thought to himself. Carson lowered him voice and gently approached him. "John,….John its me Carson" "No, No it s hurts leave me alone…" John found himself pushing himself further and further into the corner. Carson was heart broken John was afraid of him whatever had happened to his friend he could see it was hurting him "John, its finished now, your in Atlantis" Carson tried; John was shaking looking back at Carson "Atlantis" he heard him reply as if he was trying to work out if it was true or not.

"Yes John, its me Carson" "Carson" "yes John, Carson" he replied slowly approaching. John was confused, this person was getting closer and it didn't look like Carson so he raised his fist to hit him but as the man got closer the image flickered as Carson got close enough and John went to strike the face suddenly changed and there was Carson with the look of fear on his face and his fist an inch from his face. "Oh, God …Oh God" he found himself repeating "I'm so sorry" and felt to the floor breaking down completely. Carson pulling himself out of the shock his friend had nearly hit him, bent down and pulled John close into him, completely feeling the walls breaking down and the tears wetting his jacket as John began to cry. The nurses stood there unsure of what to do, it was the colonel in scrubs sat on the floor with their chief medical officer hugging him and they had never seen him like this before, realising he had an audience Carson turned "look can one of you bring me a sedative and the rest of you take a break ok" the crowd dispersed and Carson found himself handed a needle. "Thanks Nellie , take a break ok we will be fine.." "if your sure" Yeah lass get yourself a cuppa, and if you see Rodney could you tell him to come down here please I think John would appreciate a friend" knowing John would hate the audience as much as himself he found himself in a empty infirmary with just John "John, I'm going to give you a sedative ok…" no reply "it will help you relax and take the pain away ok" Carson waited knowing John was in a complete breakdown "John I'm going to do it now ok" "ok" John whispered back. Carson inserted the needle into John arm and he suddenly felt John's body go lax, keeping hold of him Carson just held him knowing that someone would return soon and help him get him into bed.

John felt himself slipping into a deep sleep, as he felt the needle go into his arm John started to relax, he found himself just thinking about everything, Carson, his breakdown, the man who hurt him, before everything became oblivious. Was this a memory of his past? is this why he had forgotten? And why now?

Elizabeth had just settled in the office when Nellie ran in "have you seen Dr McKay?" "No why" she asked. "He's not answering his comm. It's the colonel he's had an episode and Dr Beckett thinks it would a good idea for Rodney to be there when he wakes up" Elizabeth looked confused she knew John had collapsed but what was going on. "Carson this is Elizabeth" " Yes Elizabeth a little busy right now" "Carson what's going on I've got Nellie in here telling me John has had some sort of Episode is he alright" she found herself worrying "Look Elizabeth its best we don't talk right now I've got John he's been sedated but he's not good I think we better discuss this when I've got him sorted, could you just make sure Rodney comes to the infirmary ok" "ok" signing of Elizabeth quickly contacted Rodney on the com. "Dr McKay this is Elizabeth Weir can you please report to the infirmary immediately". Hoping to god Rodney wouldn't ignore her she sat in the office awaiting further news on John's condition.


	8. Chapter 8

Chapter 8

Thinking to her self, Alison thought it might be interesting to head over to the infirmary and maybe introduce herself to the Colonel what harm could it do he would either recognise her or he would just think she was another member of the female species taking an interest in his sex life.

First she had to grab something to eat she was starving and had worked up quite an appetite, heading down to the mess hall to grab something to eat she spied Rodney McKay acting quite nervous heading in the direction of the infirmary having what appeared to be a long winded conversation on his personal com, to whom she did not know. Quickly hiding behind the nearest pillar she listened carefully. "Yes!.. yes I got your message, I'm a busy man" "No I wasn't ignoring you?" she saw his face turn into a frown. "What do you mean Carson wants me, what for, its something serious I….I don't feel sick…ok ok I'm heading there now." Well that interesting she thought. Forgetting the issue of food Alison followed behind not letting Dr McKay catch her following him, she could hear him mumbling to himself "God I'm sick. What other reason could that witch doctor want me." "God I'm dying ….I mean he's told me everything before…" the realisation that it could be serious just seemed to spur him on and make go faster causing her to lose him around the corner.

Well that was interesting she thought as she decided to turn back towards the infirmary and see what was going on with that frustrating man, she could kill two birds with one stone and best of all get some fun blackmail material and Dr McKay may just leave her be.

Carson had just managed to move the colonel to the sofa in his office when Rodney came rushing into the infirmary shouting 'Carson, Carson … where are ya?' Carson could hear Rodney thank god! He thought he had sent most of his staff away for a few hours whilst he sorted out the colonel but it seemed whilst he was waiting for Rodney to come to the infirmary there had been a medical emergency, so he told majority of his staff to head over. "Rodney over here, I'm in the small office" what you doing in there?" "Rodney shut up" Rodney entered the office and found Carson looking physically exhausted resting at his desk and as he turned he saw the colonel asleep on the sofa where Carson had placed him. "What happened? Is he ok?" Carson looked at him and could see his genuine concern. "I'll explain in a minute just help me get up" Rodney looked at him frowning "its hard work you know moving a heavy man such as the colonel on your own I'll have you know" Rodney looked around noticing there was no one around "where's your staff". "I sent them out whilst I dealt with the colonel he wasn't well and well there was a medical emergency so most of them are over there" "oh …Gods he was heavy".

Carson and Rodney left the office and headed in the main infirmary leaving the colonel asleep in the office. "So what's going on" asked Rodney observing everything around him "the colonel had an episode earlier, I don't know what happened it was like I wasn't there" Rodney frowned, thinking about it Rodney remembered the conversation with John from earlier " could it have something to do with the chair and him blacking out earlier" "I don't know…..but Rodney you need to know that John said something about being sexually assaulted" Rodney looked shocked looking towards the office and his best friend "did he tell you who it was" "no Rodney but he didn't seem to know where he was and then he nearly hit me" Rodney couldn't help but grasp. "Are you ok?" "yeah he seemed to pull out of it, but when he saw what he had nearly done he broke down Rodney…..God it was heartbreaking I didn't know what to do". Both men became silent like they were thinking about what to do next, not realising that the whole conversation had just been heard by a third individual hiding away in the shadows of the room.

Rodney didn't know what to think, his best friend he had just learnt had been raped and that the episode from the chair may have inadvertently cause him to remember this event, God it was all his fault. "I should never of asked him to sit in the chair" "Rodney you didn't know this was going to happen" "I know but I still feel bad he's the strongest person I know things like this aren't suppose to happen to him" Carson placed a supportive hand upon his shoulder showing he understood. "Come on he will be awake soon I think he going to need your support" Rodney nodded returning into the office to wait for his best friend to wake up.

Alison wasn't sure of what to make of the information she had just heard, sneaking away she headed back to her room taking in the fact that the colonel was experiencing such pain, not only that it only further solidified the evidence that John Sheppard was in fact John Sinclair. "Oh God …." She whispered as she was left with the knowledge that he was alive after all this time.


	9. Chapter 9

Chapter nine

Alison woke in her room early the next morning, she couldn't even remember how she got there. The beeping of an alarm bought her back to the present when she remembered that she was supposed to have summitted a report to Rodney Mackey hours ago by the sound of the shouts now apparent in her earpiece. 'where the hell are you?' she could hear the annoyance and the slight sound of tiredness down the ear piece 'Dr Mckay i'm so sorry i just lost track of time' which was true she didn't expect to find out her best friend was alive and well and she certainty didn't expect to find out why he went missing all those years ago. Getting back to the present and the current conversation well one sided abusive rant she quickly apologised and managed to get a word in about meeting up with him and passing over her rearch results which seemed to calm him slightly. After managing to get away she had a quick shower before heading to meet with her supervisor.

John woke to find himself lay comfortably on a couch rather then a bed he was sure he was lay on before he fell asleep. Now wanting to disturb anyone or get disturbed he quickly sat up with the intention to escape back to his room without a certain scottish doctor realising he was gone. Why he was here would have to wait. Getting up he had a sudden rush of pain in his left side had he manage to hurt himself somehow from his move from the bed to here. Not thinking to much about it he moved towards the door before he was hit with an image of him swinging a fist at the doc. Confused he continued to move towards the door where this thought had come from and if he had actually done this. He didn't get to far before a voice called him ' excuse him colonel and where do you think your going' turning to face who he knew was going to be his jailer for the next few hours John turned round and put on his charming face in hopes it would be enough to get Carson let him out of here, for some reason the infirmary felt more closed in then usual. It was Carson face however, that seemed to say there more wrong then he thought. Carson stared at the colonel he appeared to be tired but otherwise showed no signs of the behaviour from earlier which was a worry in its self , Carson could sense that John was picking up these signals because the cheeky grin that he had was disappearing quickly. 'Carson, whats wrong?' 'colonel we need to talk!' was all Carson said before he gestured for him to go his office. Not liking this john led the way with Carson following closely behind , 'with that look doc it can't be good!' indicated John as he took a seat on the very sofa he had woke up on.

Taking two minutes to compose him Carson began, 'John what can you tell me about what happened last night' looking confused John just highlighted how he was in the chair and then became ill so he came to the infirmary and some how woke up on the chair even though he was sure he was asleep in one of the beds. Taking this in Carson contniued to listen closely to what John was telling him only that he couldn't remember anything about the incident with the flashback. ' John don't you remember waking up and telling me to leave you alone' 'no' replied john begining to look concerned ' what about trying to attack me' john started to feel sick 'no no no' was all carson heard him say before he saw him dart over to the nearest bin and throw up. Carson rushed over 'John calm down , i'm ok,i'm ok' john turned and looked at him with soft eyes ' i'm so sorry ' Carson smiled and calmy helped him back to the chair ' it's not your fault JOhn you were having some sort of flashback and you lashed out' 'flashback, flashback about what' he asked. Carson looked at john 'john you don't remember' 'no' was the only reply. Carson knew he had to approach this gently. 'john your were remembering someone hurting you' he informed him gently ' what do you mean hurting me, hurting me how' Carson sighed he knew this was coming ' john look at me, you were remembering being raped, thats why you lashed out' john looked at him with disbelieving eyes ' no i can't of been, something like that i would know' Carson could see John was looking confused and quite disturbed. Carson gently placed his hand on his shoulder 'its ok john we'll work it out' then leaving john to his thoughts.


	10. Chapter 10

Chapter Ten

John wanted to forget everything that happened within the last few days it was like one huge never ending nightmare. Standing in front of the mirror he stared back at his tired looking face and wondered if it was a good idea attending work today, it would be so easy to contact Lorne and ask him to cover his duties. He was being plagued with images of a man's face that made his body shiver in fear and revulsion and he didn't want people to see how distracted he was.

Sighing he quickly made a decision, washing the weariness from his face with a splash of water he headed out of the bathroom into his room and donned his uniform. Taking a moment to assess he looked presentable he then grabbed his gun on his went out of the door and he briskly headed to his office to meet with Lorne.

Alison was late up again, with all that had happened she had struggled to sleep with the thoughts of John Sheppard plaguing her mind. Feelings as rough as she looked she ran down the corridor hoping to get to the lab before Rodney noticed she wasn't there, not noticing the distracted Colonel now in her sightline until she crashed into him.

'Ouch' she heard from the figure that was underneath her groaning in discomfort. Collecting herself and suddenly realising the compromising position she was now in, she found herself clumsily trying to get up without success.

'Well I could get used to this' she heard the man underneath mumble has she fell back onto his body, suddenly realising that she recognised the voice she stopping moving and stared in to the green eyes of Colonel John Sheppard. She had thought about approaching him but to literally fall onto him was not in the game plan. Sensing that the woman that had managed to take him out was now intensely staring at him John started to feel a little uncomfortable.

Alison sensing the sudden tenseness in John's body she quickly gathered herself together and apologised to now deeply embarrassed Colonel. 'Oh I am sorry' pushing herself up much to the relief of John who was till lay on the floor in a leap, 'let me help you' she insisted.

Taking the hand of the woman in front of his him she steadied herself and pulled the now bemused man to his feet, 'Well thanks doc didn't expect that today' brushing his uniform down. Checking he had managed to clear any evidence of the event he held out his hand to the small scientist now stood in front of him.

'Colonel John Sheppard, I don't believe we have met' waiting for her to shake it. 'I know' she replied to see his eyebrows raise in surprise 'I was at the meeting when you introduced yourself to the newbies'. 'OH' he mouthed, taking his hand and shaking it firmly 'Alison Mallory' she announced 'I work in Doctor McKay's department. 'Poor you' he laughed to which she giggled in response.

Both looked surprised at that but shrugged it off, 'well doc I have to get going I going to be late' not wanting to let go of her hand and not truly understanding why. Realising that she was now behind scheduled, she quickly agreed and also muttered her own apologises also releasing her hand reluctantly from his hold. Has they both turned to go in their own respective directions he quickly turned and called back to her before he could stop himself.

'Alison' he called, upon hearing her name she turned expectantly to John 'Yes' she replied.

'How about we catch up for lunch and we can formally introduce ourselves better' he asked, Alison not wanting to lose out on getting to know the man she believed to be her long lost friend she agreed.

'How about I meet you at Rodney's Lab at noon' he asked, 'that will be fine colonel I see you then' she replied.

'Cool Catch ya later doc' turning to leave and walking briskly away before Alison could change her mind.

'Well that was unexpected' she whispered to herself before checking her watch. 'OH shit' she shouted before running in the direction of the lab and a now pissed of Rodney McKay.


	11. Chapter 11

Chapter eleven

Alison was surprised she had expected Rodney to be more annoyed then he was when she turned in late, she somehow suspected a certain colonel had something to do with that. He just seemed to stare at her with a frustrated glare and prompted her to get to work.

It was fast approaching noon and it wasn't long before she heard the snarky voice of Doctor Mckay obviously making it clear that he was not happy. 'What do you mean you're taking her to lunch, she not finished yet' she heard as his voice appeared to be getting higher. It was only then when she heard 'Sheppard you are not using your Kirkiness on my scientist, I got enough problems without you corrupting them with your charms', did she know the colonel had arrived as promised.

Putting her tablet down, she walked over to the now blood red Rodney pointing his finger at a very bemused Colonel. 'Rodney it's just lunch, I am not going to suddenly declare my undying love for her' he replied. 'I don't care your just doing this to annoy me aren't you, oh! OH! I can see it now let's get Rodney to go mad and collapse of high blood pressure so we can all laugh'. 'Rodney I was going to invite you too, being by best buddy and all' to which appeared to calm him 'oh' Rodney blustered. 'And there's cookies ' John continued 'I checked with cook' he continued, hearing cookies Rodney quickly informed Radek he was going to lunch and marched out of the lab.

Alison watched the whole event in quiet watching how John and Rodney interacted and couldn't understand how two men who were completely different were such good friends. Realising she was now being watched, Radek approached her 'you're wondering how their relationship works aren't you' he asked 'well yes' she responded. 'I mean the colonel is the colonel and Rodney what can I say' she highlighted like it was obvious.

'Well you won't be the first to say that' he expressed 'John keeps Rodney grounded and approachable and as you see John is able to manipulate Rodney very well yes' smirking at the events unfolding before them. She smirked back and quickly tuned into John's voice who was now calling out to her. 'Well doc you ready it appears it won't be just us you ok with that' he asked politely 'yeah sure that fine' she responded before she was cut off by the voice of Rodney calling 'Sheppard hurry up' from the corridor'. 'Well you heard his highest, gets get going' he smirked to the now giggling scientist as walked out of the lab together.

Over the next few weeks this became a regular occurrence and Alison found herself getting to know John friends very well. She found Ronan and Telya's company to be very stimulating and she found that she enjoyed lunch with John and the others including Rodney and it was the highlight of her day.

John found himself feeling exactly the same but he was also noting that the nightmares were getting worse the more time he spent with Alison. Not only had that he felt a strange sense of familiarity like they had met before. John hated to say it but when he lost his memory all those years ago he had felt no desire to seek out his past, but in recent weeks he now felt completely different. Deciding that he needed to learn more John one day after having lunch with Alison and his teammates locked himself in his office and accessed Alison Mallory files, it was time he learnt more about this woman.

The files appeared to show nothing out of the ordinary, she was a scientist and he could see why she was selected for Atlantis she was brilliant. Digging deeper he suddenly came across a name that suddenly caused him to freeze, 'Macgver' and the phoenix foundation. Not knowing why he reacted the way he did, John could only figure that the man was somehow linked to his past. Searching he managed to find a picture hoping that it would trigger a memory, but all it seemed to do what cause further frustration. 'Damn' he cursed slamming his hand down hard on the desk, not realising that Lorne at that point had just entered the room. 'You ok sir' a concerned Lorne asked John 'Yeah! Sorry was just checking something and came up empty' 'ok' Lorne replied 'are you sure there is nothing I can help you with' he asked calmly.' 'No, no don't worry its nothing' closing the computer down John decided to go for a walk leaving a very concerned Lorne wondering what to do about his CO who was acting very strange.


End file.
